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removing dependance on jobQueue == gsa 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5889 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-05-27 10:12:09 +00:00
parent a77ca2d36a
commit 549172af10
1 changed files with 5 additions and 5 deletions
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10
scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
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@ -31,13 +31,13 @@ class ManySampleUGPerformanceTesting extends QScript {
this.jarFile = gatkJarFile;
this.intervals = List(new File(TARGET_INTERVAL));
this.reference_sequence = referenceFile;
this.jobQueue = "gsa";
this.memoryLimit = 8
//this.jobQueue = "gsa";
this.memoryLimit = 4
//this.commandDirectory = new File("results");
}
def script = {
for (nSamples <- if ( EXOME_NSAMPLES) List(1, 2, 4, 8, 16, 32, 60) else List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900) ) {
for (nSamples <- if ( EXOME_NSAMPLES) List(1, 2, 5, 10, 25, 50, 100, 200, 300, 400, 500) else List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900) ) {
// for (nSamples <- List(10)) {
val sublist = new SliceList(nSamples)
val mergeSublist = new MergeBAMs(sublist.list)
@ -69,7 +69,7 @@ class ManySampleUGPerformanceTesting extends QScript {
}
class Index(bamIn: File) extends SamtoolsIndexFunction {
this.jobQueue = "gsa"
//this.jobQueue = "gsa"
bamFile = bamIn
}
@ -98,7 +98,7 @@ class ManySampleUGPerformanceTesting extends QScript {
class SliceList(n: Int) extends CommandLineFunction {
@Output(doc="foo") var list: File = new File("bams.%d.list".format(n))
def commandLine = "head -n %d %s > %s".format(n, FULL_BAM_LIST, list)
this.jobQueue = "gsa";
//this.jobQueue = "gsa";
}
}